title: Molecular dynamic and docking interaction study of Heterodera glycines serine proteinase with Vigna mungo proteinase inhibitor.
abstract: Many plants do produce various defense proteins like proteinase inhibitors (PIs) to protect them against various pests. PIs function as pseudosubstrates of digestive proteinase, which inhibits proteolysis in pests and leads to amino acid deficiency-based mortality. This work reports the structural interaction studies of serine proteinase of Heterodera glycines (SPHG) with Vigna mungo proteinase inhibitor (VMPI). 3D protein structure modeling, validation of SPHG and VMPI, and their putative protein-protein binding sites were predicted. Protein-protein docking followed by molecular dynamic simulation was performed to find the reliable confirmation of SPHG-VMPI complex. Trajectory analysis of each successive conformation concludes better interaction of first loop in comparison with second loop. Lysine residues of first loop were actively participating in complex formation. Overall, this study discloses the structural aspects and interaction mechanisms of VMPI with SPHG, and it would be helpful in the development of pest-resistant genetically modified crops.
authors.affiliation: Division of Applied Science & IRCB, Indian Institute of Information Technology, Deoghat, Jhalwa, Allahabad, 211012, India. shiva@iiita.ac.in
authors.forename: C V S Siva
authors.initials: CV
authors.lastname: Prasad
authors.forename: Saurabh
authors.initials: S
authors.lastname: Gupta
authors.forename: Alex
authors.initials: A
authors.lastname: Gaponenko
authors.forename: Murlidhar
authors.initials: M
authors.lastname: Tiwari
mesh_terms: D000818:Animals; D000969:Antinematodal Agents / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D003198:Computer Simulation; D007887:Fabaceae / Q000378:metabolism*; D008956:Models, Chemical; D008958:Models, Molecular; D009348:Nematoda / Q000201:enzymology*; D011480:Protease Inhibitors / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D057057:Serine Proteases / Q000737:chemistry*
chemical_list: D000969:Antinematodal Agents; D011480:Protease Inhibitors; D057057:Serine Proteases